Align 3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate BPHYT_RS20960 BPHYT_RS20960 dihydrofolate reductase
Query= uniprot:A0A1X9ZCD3 (315 letters) >FitnessBrowser__BFirm:BPHYT_RS20960 Length = 320 Score = 134 bits (337), Expect = 3e-36 Identities = 89/261 (34%), Positives = 135/261 (51%), Gaps = 13/261 (4%) Query: 43 AITVRSATKVRKELIDAVPN-IKLIGRGGVGMDNIDVEYARSQGINVVNTPAASSLSVAE 101 A+ + + ++ E I A+P+ +K+I G D++DV AR +GI V N P A + A+ Sbjct: 52 AVLIGKKSGLQAEHIAALPSTVKIIANASAGFDHMDVAAARERGIVVTNAPDALTECTAD 111 Query: 102 LVFSHLFTGIRFLQDANRKMPVEGSTQFNNLKKAYAKGTELSGKTIGIIGFGRIGRATAK 161 + R + R M F + GT ++GKT+GI+GFGRIGRA AK Sbjct: 112 FSLLLVLAACRRASEYERIMRNGWGKSFGMTEML---GTRVNGKTLGIVGFGRIGRAVAK 168 Query: 162 VALGLGMNVLAYDLYPSESEITLEFQGGKSVSIPIKTVSLDEVITGSDFFSLHTPFADKP 221 A G GM V+ D+ + + +LE G + SLDE++ +LH P P Sbjct: 169 RAQGFGMRVIYTDI--NRAAASLE-NGATFYN------SLDEMLPHCQVLTLHVPGGGVP 219 Query: 222 ILGAEEFAKMKNGVGIVNCSRGGTIDELALIDALNSGKVSFAGLDVFDNEPTPLAEILTH 281 ++ EFA + G VN +RG +DE AL +AL SG + AGLDV+ NEP Sbjct: 220 LMTKREFALLPAGAVFVNAARGALVDEDALYEALTSGHLFGAGLDVYRNEPNVDKRFAGL 279 Query: 282 PKISLTPHIGASTNEAQERIG 302 + LTPH+ ++T E ++++G Sbjct: 280 DNVFLTPHMASATMETRDQMG 300 Lambda K H 0.316 0.135 0.374 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 234 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 315 Length of database: 320 Length adjustment: 27 Effective length of query: 288 Effective length of database: 293 Effective search space: 84384 Effective search space used: 84384 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory